James Hutchins
Bioinformatics links and tools
General Bioinformatics Tools
DNA: OligoCalc • OligoAnalysis • Reverse Complement Tool
NCBI Primer-BLAST • EMBOSS suite • EMBOSS Explorer
Peptides / Proteins: ProteinCalc
This page is currently being reorganised for consistency with my review article:
Hutchins, JRA (2014) “What’s that gene (or protein)? Online resources for exploring functions of genes, transcripts, and proteins” Mol. Biol. Cell 25:8 1187-1201; doi:10.1091/mbc.E13-10-0602. Invited Technical Perspective article.
Abstract (journal website) • PubMed entry • Google Scholar entry
Download PDFs of Main Article and Supplementary Materials
Download PDF of updated Supplementary Document
1. Sequence
Gene & protein databases
UniProt • Ensembl • NCBI Gene • NCBI Protein • TGI Gene Index
Genome browsers
UCSC Genome Browser • Ensembl
Species-specific databases
HGNC (human) • MGD (mouse) • SGD (S.cerevisiae) • PomBase (S.pombe)
FlyBase (Drosophila) • TAIR (Arabidopsis) • AspGD (Aspergillus)
WormBase (C.elegans) • ZFIN (zebrafish) • dictyBase (Dictyostelium)
RGD (rat) • Xenbase (Xenopus) • ANISEED (Ascidians)
2. Functions
Literature: PubMed • Google Scholar • Scirus • iHOP • Textpresso
Online Mendelian Inheritance in Man (OMIM)
Ontology terms: Gene Ontology (GO) • QuickGO • PANTHER
MitoCheck Database (www.mitocheck.org) - based on human genes but queryable using non-human gene symbols, this is a functional genomic database allowing access to video-microscopy data from multiple genome-wide RNAi screens.
Enzyme info
BRENDA • IntEnz • EBI Enzyme Portal
Reactions & Signalling Pathways
BioCarta Pathways (hosted by the NCI's Cancer Genome Anatomy Project)
3. Homologues & Evolution
HomoloGene • TreeFam
4. Expression
Gene Expression Omnibus (GEO) • ArrayExpress • Gene Expression Atlas
At the protein level: Human Protein Atlas
5. Composition: domains, motifs & 3D structure
Protein domains & sequence motifs
Domains & motifs:
Conserved Domain Database (CDD)
ELM (Eukaryotic Linear Motif) functional site prediction
ANNIE (protein sequence annotation and interpretation environment)
DASty (annotation with Distributed Annotation System): now unfortunately retired.
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Protein 3D Structure
Protein Data Bank (PDB) • PDBsum • MMDB / NCBI Structure
6. Interaction Partners
IntAct • STRING • BioGRID • IMEx Consortium
7. Post-translational Modifications
Databases of experimentally-determined PTMs:
PhosphoSitePlus • Phospho.ELM • PHOSIDA • dbPTM
PTM prediction sites:
8. Genetic variations & disease
Disease Association: Genetic Association Database • KEGG Disease
9. Inhibitors & druggability
Chemical & drug databases:
Searchable by drug targets:
PubChem Bioassay • ChEMBL • canSAR
Comparative Toxicogenomics Database (CTD)
"Druggability": DrugEBIlity
10. Overview
Cross-database searches
EBI Gene & Protein Summary • GeneCards (human genes)
Human Protein Reference Database
Bioinformatic Harvester - now retired
Dataset-wide Analysis Tools
Compare two lists • Compare three lists
Retrieval of GO and other terms & properties:
UniProt: "Retrieve" (UniProt codes) • "ID Mapping" (non-UniProt IDs)
Batch display of protein domains:
Over-representation analysis:
DAVID • GeneCodis • GenePattern